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protocols::loops Namespace Reference

Namespaces

 filters
 
 loop_closure
 
 loop_mover
 
 loops_definers
 

Classes

class  EXCN_Loop_not_closed
 
class  FoldTreeFromLoops
 
class  FoldTreeFromLoopsCreator
 
class  GuardedLoopsFromFile
 This class ensures that the Loops object that is needed to run any of the various forms of loop modeling is correctly initialized from a Pose. If the residues specified from a loops file have not been resolved into the residue indices for a Pose, then this class will die with an assertion failure. More...
 
class  JSONFormattedLoopsFileReader
 
class  Loop
 single loop definition More...
 
class  Loop_lt
 used to sort Loops by start-res More...
 
class  LoopFromFileData
 
class  LoopMoverFactory
 Create LoopMover Reporters. More...
 
class  Loops
 
class  LoopsFileData
 
class  LoopsFileIO
 
class  LoopsFileLoader
 LoopsFileLoader constructs a LoopsFileData instance from data provided by the ResourceManager. More...
 
class  LoopsFileLoaderCreator
 LoopsFileLoaderCreator allows the ResourceLoaderFactory to create a LoopsFileLoader instance. More...
 
class  PoseNumberedLoopFileReader
 
class  RationalLoopComparator
 Orders loops by start position. More...
 
struct  SerializedLoop
 Bare-bones representation of a loop. More...
 

Typedefs

typedef
utility::pointer::shared_ptr
< FoldTreeFromLoops
FoldTreeFromLoopsOP
 
typedef
utility::pointer::shared_ptr
< FoldTreeFromLoops const > 
FoldTreeFromLoopsCOP
 
typedef
utility::pointer::shared_ptr
< Loop
LoopOP
 
typedef
utility::pointer::shared_ptr
< Loop const > 
LoopCOP
 
typedef utility::vector1
< SerializedLoop
SerializedLoopList
 
typedef
utility::pointer::shared_ptr
< Loops
LoopsOP
 
typedef
utility::pointer::shared_ptr
< Loops const > 
LoopsCOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileData
LoopsFileDataOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileData const > 
LoopsFileDataCOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileIO
LoopsFileIOOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileIO const > 
LoopsFileIOCOP
 
typedef
utility::pointer::shared_ptr
< GuardedLoopsFromFile
GuardedLoopsFromFileOP
 
typedef
utility::pointer::shared_ptr
< GuardedLoopsFromFile const > 
GuardedLoopsFromFileCOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileLoader
LoopsFileLoaderOP
 
typedef
utility::pointer::shared_ptr
< LoopsFileLoader const > 
LoopsFileLoaderCOP
 

Enumerations

enum  ResidueIdentifier { start =1, stop, cut_point, number_of_residue_identifiers =cut_point }
 The following enumerators are used for parsing JSON formatted loop files. More...
 
enum  LoopConfiguration {
  extras =number_of_residue_identifiers + 1, resSeq, iCode, chainID,
  skip_rate, extend, use_pose_numbering, number_of_configuration_keywords =use_pose_numbering
}
 

Functions

static basic::Tracer TR ("protocols.loops.FoldTreeFromLoopsWrapper")
 
static basic::Tracer tr ("protocols.loops.Loop")
 
std::ostream & operator<< (std::ostream &os, Loop const &loop)
 
void loopfinder (core::pose::Pose &pose, loops::Loops &loops)
 
static basic::Tracer tr ("protocols.loops.LoopMoverFactory")
 
static basic::Tracer tr ("loops")
 
std::ostream & operator<< (std::ostream &os, const Loops &loops)
 
static basic::Tracer tt ("protocols.loops.loops_main")
 
void read_loop_fragments (std::vector< core::fragment::FragSetOP > &frag_libs)
 
void read_loop_fragments (utility::vector1< core::fragment::FragSetOP > &frag_libs)
 
void fold_tree_from_loops (core::pose::Pose const &pose, Loops const &loops, core::kinematics::FoldTree &f, bool terminal_cutpoint=false)
 the main function for perform loop modeling More...
 
void set_single_loop_fold_tree (core::pose::Pose &pose, Loop const &loop)
 
void set_loop_cutpoint_in_pose_fold_tree (Size const new_cutpoint, pose::Pose &pose, Size const loop_begin, Size const loop_end)
 
void remove_cutpoint_variants (core::pose::Pose &pose, bool force)
 
void add_cutpoint_variants (core::pose::Pose &pose)
 Add cutpoint variants to all the cutpoints in a Pose. More...
 
void add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)
 Add cutpoint variants around a single cutpoint (defined by a Loop). More...
 
void add_single_cutpoint_variant (core::pose::Pose &pose, const core::uint cutpoint)
 Add cutpoint variants around a single cutpoint (defined by residue number). More...
 
void loops_set_move_map (pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, Real neighbor_dist)
 
void loops_set_move_map (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, core::Real neighbor_dist, bool const allow_omega_move, bool const allow_takeoff_torsion_move)
 create a MoveMap for use of minimization based on loop definition (wrapper) More...
 
void loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm)
 create a MoveMap for use of minimization based on loop definition More...
 
void loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm, bool const allow_omega_move, bool const allow_takeoff_torsion_move)
 
core::kinematics::MoveMapOP move_map_from_loops (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
 Create a new MoveMapOP for use in minimizing the given loop. More...
 
core::kinematics::MoveMapOP move_map_from_loop (core::pose::Pose &pose, Loop const &loop, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
 Create a new MoveMapOP for use in minimizing the given loop. More...
 
void set_move_map_for_centroid_loop (Loop const &loop, core::kinematics::MoveMap &mm)
 
void add_loop_flank_residues_bb_to_movemap (Loops const &loops, core::kinematics::MoveMap &mm, core::Size flank_size=2)
 add flank stem residues to the loop movemap More...
 
void ccd_close_loops (core::pose::Pose &pose, Loops const &loops, core::kinematics::MoveMap const &mm)
 close loops by the CCD mechanism More...
 
void select_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary in a sequence map. More...
 
utility::vector1< boolselect_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary in a sequence map. More...
 
void select_loop_residues (core::pose::Pose const &pose, Loop const &loop, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary for one loop. More...
 
utility::vector1< boolselect_loop_residues (core::pose::Pose const &pose, Loop const &loop, bool const include_neighbors, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary for one loop. More...
 
void filter_loop_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > &map, Loops const &loops, core::Real &dist_cutoff)
 filter set of loop neighbors to a certain CB distance Takes distance from selection to neighbors to trim neighbors. More...
 
void extend_sequence_mapping (pose::Pose const &pose, id::SequenceMapping &mapping, std::string &source_seq, std::string &target_seq)
 
void apply_sequence_mapping (pose::Pose &pose, std::string const &target_seq, id::SequenceMapping const &start_mapping)
 
void trim_back_sequence_mapping (core::id::SequenceMapping &mapping, std::string const &source_seq, std::string const &target_seq, core::Size const min_loop_size)
 Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed. More...
 
bool set_secstruct_from_psipred_ss2 (core::pose::Pose &pose, std::string const &filename=std::string())
 helper function to set secondary structure of a Pose from an external file. More...
 
bool set_secstruct_from_dssp (core::pose::Pose &pose, std::string const &filename)
 another helper function to set secondary structure of a Pose from an external file. More...
 
void idealize_loop (core::pose::Pose &pose, Loop const &loop)
 
void set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
 
void remove_missing_density (core::pose::Pose &pose, Loop const &loop)
 
core::Real native_loop_core_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose, loops::Loops loops, int &corelength)
 
Real loop_rmsd_with_superimpose (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 As above but actuall superimposes the non-loop part. More...
 
Real loop_rmsd_with_superimpose_core (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, Loops const &core, bool CA_only=false, bool bb_only=true)
 As above but actually superimposes only the core part (in case there are multiple loops...) More...
 
Real loop_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 calculate rmsd of loop residues with repect to native (template aligned) More...
 
Real loop_local_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops)
 calculate rmsd of loop residues with repect to native (loop fit) More...
 
static basic::Tracer tr ("protocols.loops.LoopsFileIO")
 
void validate_loop_start_stop (bool prohibit_single_residue_loops, core::Size start, core::Size stop, std::string const &filename, core::Size linecount)
 Checks if there is a problem with the beginning and ending residues defined in a loops file. More...
 
core::pose::ResidueIndexDescriptionCOP make_rid_posenum (std::string const &fname, core::Size lineno, core::Size resnum)
 
std::ostream & operator<< (std::ostream &os, const LoopsFileIO &)
 
static basic::Tracer TR ("protocols.loops.make_loops", t_info)
 
void add_loop (Size seg_begin, Size seg_end, pose::Pose const &pose, loops::Loops &loops)
 
void loops_around_residues (loops::Loops &loops, pose::Pose const &pose, vector1< Size > const &residue_indices, Size gapsize, Size extend)
 add a set of loops 'built' around the provided residue indices More...
 
void loops_around_residues (Loops &loops, core::pose::Pose const &pose, utility::vector1< core::Size > const &residue_indices, core::Size gapsize=6, core::Size extend=2)
 add a set of loops 'built' around the provided residue indices More...
 
void fix_with_coord_cst (Loops const &rigid, core::pose::Pose &pose, bool bCstAllAtom, utility::vector1< core::Real > &weights)
 
void select_loop_frags (loops::Loops const &loops, core::fragment::FragSet &source, core::fragment::FragSet &loop_frags, Size shorten)
 get frags that are fully within the Loop — shorten(=true/false) frags that are close to the end of loops. More...
 
void safe_set_extended_torsions_and_idealize_loops (const protocols::loops::Loops &loops, core::pose::Pose *pose)
 Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops. More...
 
void set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops)
 
void addScoresForLoopParts (core::pose::Pose &pose, loops::Loops loops, const core::scoring::ScoreFunction &scorefxn, core::pose::Pose &native_pose, core::Size nloops)
 
loops::Loops compute_ss_regions (core::Real max_loop_frac, core::Size min_length, core::fragment::SecondaryStructure const &ss)
 
core::scoring::ScoreFunctionOP get_cen_scorefxn ()
 
core::scoring::ScoreFunctionOP get_fa_scorefxn ()
 
void add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)
 
LoopsOP loops_from_string (std::string const &loop_str, core::pose::Pose const &pose)
 loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop More...
 
void define_scorable_core_from_secondary_structure (core::fragment::SecondaryStructure const &ss_def, protocols::loops::Loops &scored_core)
 
protocols::loops::Loops extract_secondary_structure_chunks (core::pose::Pose const &pose, char const extracted_ss_type)
 Extract secondary structure chunks from the secondary structure. More...
 
protocols::loops::Loops split_by_resSeq (core::pose::Pose const &pose)
 
protocols::loops::Loops find_non_protein_chunks (core::pose::Pose const &pose)
 
protocols::loops::Loops split_by_resSeq (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks)
 
protocols::loops::Loops split_by_ca_ca_dist (core::pose::Pose const &pose, Loops const &input_chunks, core::Real const CA_CA_distance_cutoff=4)
 Split into separate chunks if CA-CA distance is over the cutoff. More...
 
protocols::loops::Loops remove_small_gaps (Loops const &input_chunks, core::Size gap_size=1)
 If two chunks are separated by a small gap of size <= <gap_size>, combine them. More...
 
protocols::loops::Loops remove_short_chunks (Loops const &input_chunks, core::Size min_length=3)
 Remove small chunks. More...
 
protocols::loops::Loops extract_secondary_structure_chunks (core::pose::Pose const &pose, std::string extracted_ss_types="HE", core::Size gap_size=1, core::Size minimum_length_of_chunk_helix=5, core::Size minimum_length_of_chunk_strand=3, core::Size minimum_length_of_chunk_loop=3, core::Real CA_CA_distance_cutoff=4)
 Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);. More...
 
protocols::loops::Loops extract_continuous_chunks (core::pose::Pose const &pose, core::Size const minimum_size, core::Real const CA_CA_distance_cutoff)
 
std::pair< bool, core::Sizehas_severe_pep_bond_geom_issues (core::pose::Pose const &pose, const Loop &loop, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
 Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...
 
std::pair< bool, core::Sizehas_severe_pep_bond_geom_issues (core::pose::Pose const &pose, core::Size resnum, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
 Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...
 

Variables

static const double EXT_PHI = -150
 
static const double EXT_PSI = +150
 
static const double EXT_OMG = 180
 

Typedef Documentation

typedef utility::pointer::shared_ptr< FoldTreeFromLoops const > protocols::loops::FoldTreeFromLoopsCOP
typedef utility::pointer::shared_ptr< FoldTreeFromLoops > protocols::loops::FoldTreeFromLoopsOP
typedef utility::pointer::shared_ptr< GuardedLoopsFromFile const > protocols::loops::GuardedLoopsFromFileCOP
typedef utility::pointer::shared_ptr< GuardedLoopsFromFile > protocols::loops::GuardedLoopsFromFileOP
typedef utility::pointer::shared_ptr< Loop const > protocols::loops::LoopCOP
typedef utility::pointer::shared_ptr< Loop > protocols::loops::LoopOP
typedef utility::pointer::shared_ptr< Loops const > protocols::loops::LoopsCOP
typedef utility::pointer::shared_ptr< LoopsFileData const > protocols::loops::LoopsFileDataCOP
typedef utility::pointer::shared_ptr< LoopsFileData > protocols::loops::LoopsFileDataOP
typedef utility::pointer::shared_ptr< LoopsFileIO const > protocols::loops::LoopsFileIOCOP
typedef utility::pointer::shared_ptr< LoopsFileIO > protocols::loops::LoopsFileIOOP
typedef utility::pointer::shared_ptr< LoopsFileLoader const > protocols::loops::LoopsFileLoaderCOP
typedef utility::pointer::shared_ptr< LoopsFileLoader > protocols::loops::LoopsFileLoaderOP
typedef utility::pointer::shared_ptr< Loops > protocols::loops::LoopsOP

Enumeration Type Documentation

Enumerator
extras 
resSeq 
iCode 
chainID 
skip_rate 
extend 
use_pose_numbering 
number_of_configuration_keywords 

The following enumerators are used for parsing JSON formatted loop files.

Enumerator
start 
stop 
cut_point 
number_of_residue_identifiers 

Function Documentation

void protocols::loops::add_coordinate_constraints_to_pose ( core::pose::Pose pose,
const core::pose::Pose constraint_target_pose,
protocols::loops::Loops exclude_regions 
)
void protocols::loops::add_cutpoint_variants ( core::pose::Pose pose)

Add cutpoint variants to all the cutpoints in a Pose.

References add_single_cutpoint_variant(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::loops::FoldTreeFromLoops::apply(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::antibody::GraftedStemOptimizer::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::loop_modeling::LoopMover::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::kinematic_closure::ClosureProblem::mutate_residues(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::antibody_legacy::AntibodyModeler::relax_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::loop_modeling::LoopMover::setup_fold_tree(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::loop_modeling::LoopProtocol::start_protocol().

void protocols::loops::add_loop ( Size  seg_begin,
Size  seg_end,
pose::Pose const &  pose,
loops::Loops &  loops 
)
void protocols::loops::add_loop_flank_residues_bb_to_movemap ( Loops const &  loops,
core::kinematics::MoveMap mm,
core::Size  flank_size 
)
void protocols::loops::add_single_cutpoint_variant ( core::pose::Pose pose,
const Loop &  loop 
)
void protocols::loops::add_single_cutpoint_variant ( core::pose::Pose pose,
const core::uint  cutpoint 
)
void protocols::loops::addScoresForLoopParts ( core::pose::Pose pose,
loops::Loops  loops,
const core::scoring::ScoreFunction scorefxn,
core::pose::Pose native_pose,
core::Size  nloops 
)
void protocols::loops::apply_sequence_mapping ( pose::Pose pose,
std::string const &  target_seq,
id::SequenceMapping const &  start_mapping 
)

what can we assume about the starting fold_tree??

References core::pose::add_variant_type_to_pose_residue(), core::id::SequenceMapping::all_aligned(), core::pose::Pose::chain(), core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::conformation(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::delete_residue_slow(), core::id::SequenceMapping::delete_source_residue(), core::pose::Pose::fold_tree(), core::id::SequenceMapping::insert_aligned_residue(), core::kinematics::FoldTree::is_cutpoint(), core::id::SequenceMapping::is_identity(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::num_jump(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::pose::Pose::sequence(), core::pose::Pose::set_omega(), core::id::SequenceMapping::show(), core::pose::Pose::size(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), tt(), core::conformation::Residue::type(), and core::chemical::ResidueType::variant_types().

Referenced by core::kinematics::FoldTree::delete_jump_seqpos(), and core::kinematics::FoldTree::delete_seqpos_simple().

void protocols::loops::ccd_close_loops ( pose::Pose pose,
Loops const &  loops,
kinematics::MoveMap const &  mm 
)

close loops by the CCD mechanism

This function takes a pose and loop definitions and closes each loop separately by the CCD algorithm. All parameters related to CCD are hard-coded. If one wishes more control over the options, s/he should use the CCDLoopClosureMover.

References protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::loop(), and protocols::loops::loop_closure::ccd::CCDLoopClosureMover::movemap().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), and protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop().

loops::Loops protocols::loops::compute_ss_regions ( core::Real  max_loop_frac,
core::Size  min_length,
core::fragment::SecondaryStructure const &  ss 
)
void protocols::loops::define_scorable_core_from_secondary_structure ( core::fragment::SecondaryStructure const &  ss_def,
protocols::loops::Loops scored_core 
)
void protocols::loops::extend_sequence_mapping ( pose::Pose const &  pose,
id::SequenceMapping mapping,
std::string &  source_seq,
std::string &  target_seq 
)
Loops protocols::loops::extract_continuous_chunks ( core::pose::Pose const &  pose,
core::Size const  minimum_size,
core::Real const  CA_CA_distance_cutoff 
)
Loops protocols::loops::extract_secondary_structure_chunks ( core::pose::Pose const &  pose,
char const  extracted_ss_type 
)
Loops protocols::loops::extract_secondary_structure_chunks ( core::pose::Pose const &  pose,
std::string  extracted_ss_types,
core::Size  gap_size,
core::Size  minimum_length_of_chunk_helix,
core::Size  minimum_length_of_chunk_strand,
core::Size  minimum_length_of_chunk_loop,
core::Real  CA_CA_distance_cutoff 
)

Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::begin(), protocols::loops::Loops::end(), remove_short_chunks(), remove_small_gaps(), split_by_ca_ca_dist(), and split_by_resSeq().

void protocols::loops::filter_loop_neighbors_by_distance ( pose::Pose const &  pose,
utility::vector1< bool > &  map,
Loops const &  loops,
Real dist_cutoff 
)

filter set of loop neighbors to a certain CB distance Takes distance from selection to neighbors to trim neighbors.

neighbors contains the set of potential neighbors to the loop residues given in loops. This set is reduced to only contain neighbors within dist_cutoff of any residue in loops.

References core::select::filter_neighbors_by_distance(), and core::pose::Pose::size().

Referenced by select_loop_residues().

Loops protocols::loops::find_non_protein_chunks ( core::pose::Pose const &  pose)
void protocols::loops::fix_with_coord_cst ( Loops const &  rigid,
core::pose::Pose pose,
bool  bCstAllAtom,
utility::vector1< core::Real > &  weights 
)
void protocols::loops::fold_tree_from_loops ( core::pose::Pose const &  pose,
Loops const &  loops,
kinematics::FoldTree f,
bool  terminal_cutpoint 
)

the main function for perform loop modeling

for each loop defined, add a fixed jump from the residue before loop_start and the residue after the loop_end. The cutpoint is from loop_cut. Support terminal loops, i.e., starting at residue 1 or ending at total_residue

voi/d loops_main( core::pose::Pose & pose ); construct a fold tree from loop definition

References protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::is_carbohydrate(), core::pose::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::is_upper_terminus(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), protocols::make_rot_lib::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), protocols::loops::Loops::sequential_order(), core::pose::Pose::size(), and core::pose::symmetry::symmetrize_fold_tree().

Referenced by protocols::loops::FoldTreeFromLoops::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::rbsegment_relax::RBSegmentRelax::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::LoopRefine::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::antibody::design::GeneralAntibodyModeler::extend_CDR(), protocols::abinitio::AbrelaxApplication::fold(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub(), protocols::forge::remodel::RemodelLoopMover::randomize_stage(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), set_single_loop_fold_tree(), protocols::loop_modeling::LoopMover::setup_fold_tree(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_foldtree_and_add_cutpoint_variants(), protocols::antibody::AntibodyInfo::setup_simple_fold_tree(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

core::scoring::ScoreFunctionOP protocols::loops::get_cen_scorefxn ( )
core::scoring::ScoreFunctionOP protocols::loops::get_fa_scorefxn ( )
std::pair< bool, core::Size > protocols::loops::has_severe_pep_bond_geom_issues ( core::pose::Pose const &  pose,
const Loop &  loop,
bool  check_bonds = true,
bool  check_angles = true,
core::Real  max_c_n_dis = 2.0,
core::Real  allowed_ca_c_n_deviation = 25.0,
core::Real  allowed_c_n_ca_deviation = 25.0 
)

Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1.

Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values out of this range. -JAB Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009) Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325. deviation is +/- from the min/max values of the CDL.

Parameters
Stringentcutoffs are: 1.5, 15, 15
Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References has_severe_pep_bond_geom_issues(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by protocols::antibody::design::check_cb(), protocols::antibody::AntibodyInfo::check_cdr_quality(), protocols::grafting::graft_closed(), and protocols::antibody::design::AntibodyDesignMover::run_graft().

std::pair< bool, core::Size > protocols::loops::has_severe_pep_bond_geom_issues ( core::pose::Pose const &  pose,
core::Size  resnum,
bool  check_bonds = true,
bool  check_angles = true,
core::Real  max_c_n_dis = 2.0,
core::Real  allowed_ca_c_n_deviation = 25.0,
core::Real  allowed_c_n_ca_deviation = 25.0 
)

Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1.

Values are based on the CDL. No peptide bond without severe chainbreaks or missing residues should have values out of this range. -JAB Berkholz DS, Shapovalov MV, Dunbrack RL Jr, Karplus PA (2009) Conformation dependence of backbone geometry in proteins. Structure 17: 1316-1325. deviation is +/- from the min/max values of the CDL.

Parameters
Stringentcutoffs are: 1.5, 15, 15
Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_virtual_residue(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), TR(), and core::conformation::Atom::xyz().

Referenced by has_severe_pep_bond_geom_issues().

void protocols::loops::idealize_loop ( core::pose::Pose pose,
Loop const &  loop 
)
core::Real protocols::loops::loop_local_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops 
)

calculate rmsd of loop residues with repect to native (loop fit)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of each loop after fitting it onto the reference loop and when there are multiple loops, return the mean value.

References protocols::loops::Loops::num_loop(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), and core::conformation::Residue::xyz().

core::Real protocols::loops::loop_rmsd ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
bool  CA_only,
bool  bb_only 
)

calculate rmsd of loop residues with repect to native (template aligned)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atoms(), core::sequence::end, core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), start, core::pose::Pose::total_residue(), tt(), and core::conformation::Residue::xyz().

Referenced by addScoresForLoopParts(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::simple_filters::LoopRmsdEvaluator::apply(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_five(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_four(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_one(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_three(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_two(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::debug_zero(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::get_best_neighboring_shift_RMSD_and_output_silent_file(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::is_new_cluster_center_with_working_parameters(), loop_rmsd_with_superimpose_core(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), and protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

core::Real protocols::loops::loop_rmsd_with_superimpose ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
bool  CA_only,
bool  bb_only 
)

As above but actuall superimposes the non-loop part.

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

References loop_rmsd_with_superimpose_core().

Referenced by protocols::cluster::ClusterPhilStyle_Loop::get_distance_measure().

core::Real protocols::loops::loop_rmsd_with_superimpose_core ( pose::Pose const &  pose1,
pose::Pose const &  pose2,
Loops const &  loops,
Loops const &  core,
bool  CA_only,
bool  bb_only 
)

As above but actually superimposes only the core part (in case there are multiple loops...)

pose1 is the reference and pose2 is the structure for which rmsd is calculated. The rmsd is calculated over four backbone atoms of all loop residues, assuming template regions in pose1 and pose2 are already aligned.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), protocols::loops::Loops::is_loop_residue(), loop_rmsd(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), protocols::loops::Loops::size(), core::pose::Pose::size(), and core::scoring::superimpose_pose().

Referenced by protocols::simple_filters::LoopRmsdEvaluator::apply(), and loop_rmsd_with_superimpose().

void protocols::loops::loopfinder ( core::pose::Pose pose,
loops::Loops &  loops 
)
void protocols::loops::loops_around_residues ( loops::Loops &  loops,
pose::Pose const &  pose,
vector1< Size > const &  residue_indices,
Size  gapsize,
Size  extend 
)

add a set of loops 'built' around the provided residue indices

A maximum of gapsize residues are allowed between specified residues for any given loop, loop ends are extended by extend residues, and chain discontinuity starts a new loop

Author
ashworth

References add_loop(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, extend, protocols::mean_field::min(), protocols::loops::Loops::num_loop(), core::pose::Pose::size(), and TR().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::apply().

void protocols::loops::loops_around_residues ( loops::Loops &  loops,
pose::Pose const &  pose,
vector1< Size > const &  residue_indices,
Size  gapsize,
Size  extend 
)

add a set of loops 'built' around the provided residue indices

A maximum of gapsize residues are allowed between specified residues for any given loop, loop ends are extended by extend residues, and chain discontinuity starts a new loop

Author
ashworth

References add_loop(), core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, extend, protocols::mean_field::min(), protocols::loops::Loops::num_loop(), core::pose::Pose::size(), and TR().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::apply().

LoopsOP protocols::loops::loops_from_string ( std::string const &  loop_str,
core::pose::Pose const &  pose 
)

loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop

References core::pose::parse_resnum(), and core::pose::Pose::size().

Referenced by protocols::loops::loops_definers::load_loop_definitions().

void protocols::loops::loops_set_move_map ( pose::Pose pose,
Loops const &  loops,
bool const  fix_template_sc,
core::kinematics::MoveMap mm,
Real  neighbor_dist 
)

omega backbone torsion is always fixed. phi/psi backbone torsions within the loop region are flexible. Depending on whether -fix_natsc flag, sidechain DOFs of loop residues and/or their neighboring residues in the template will be set as movable. Default neighbors are 10A CB dist from loop residues; neighbor_dist can be used to further filter the neighbors. This is a wrapper function which determine moveable sidechains and then call actual loop_set_move_map function to set up move map properly

References loops_set_move_map().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::setup_movemap(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors().

void protocols::loops::loops_set_move_map ( pose::Pose pose,
Loops const &  loops,
bool const  fix_template_sc,
core::kinematics::MoveMap mm,
Real  neighbor_dist,
bool const  allow_omega_move,
bool const  allow_takeoff_torsion_move 
)
void protocols::loops::loops_set_move_map ( Loops const &  loops,
utility::vector1< bool > const &  allow_sc_move,
core::kinematics::MoveMap mm 
)

create a MoveMap for use of minimization based on loop definition

References loops_set_move_map().

void protocols::loops::loops_set_move_map ( Loops const &  loops,
utility::vector1< bool > const &  allow_sc_move,
core::kinematics::MoveMap mm,
bool const  allow_omega_move,
bool const  allow_takeoff_torsion_move 
)
core::pose::ResidueIndexDescriptionCOP protocols::loops::make_rid_posenum ( std::string const &  fname,
core::Size  lineno,
core::Size  resnum 
)
core::kinematics::MoveMapOP protocols::loops::move_map_from_loop ( core::pose::Pose pose,
Loop const &  loop,
bool const  fix_template_sc,
core::Real  neighbor_dist,
bool const  flanking_residues 
)

Create a new MoveMapOP for use in minimizing the given loop.

Wrapper around loops_set_move_map which works on a single loop object and returns a MoveMapOP. See the detailed documentation for loops_set_move_map for more information about the generated MoveMap.

References protocols::loops::Loops::add_loop(), and move_map_from_loops().

core::kinematics::MoveMapOP protocols::loops::move_map_from_loops ( core::pose::Pose pose,
Loops const &  loops,
bool const  fix_template_sc,
core::Real  neighbor_dist,
bool const  flanking_residues 
)

Create a new MoveMapOP for use in minimizing the given loop.

Wrapper around loops_set_move_map which works on a single loop object and returns a MoveMapOP. See the detailed documentation for loops_set_move_map for more information about the generated MoveMap.

References add_loop_flank_residues_bb_to_movemap(), and loops_set_move_map().

Referenced by move_map_from_loop().

core::Real protocols::loops::native_loop_core_CA_rmsd ( const core::pose::Pose native_pose,
const core::pose::Pose pose,
loops::Loops  loops,
int &  corelength 
)
std::ostream & protocols::loops::operator<< ( std::ostream &  os,
Loop const &  loop 
)
std::ostream& protocols::loops::operator<< ( std::ostream &  os,
const Loops &  loops 
)
std::ostream& protocols::loops::operator<< ( std::ostream &  os,
const LoopsFileIO &   
)
void protocols::loops::read_loop_fragments ( std::vector< core::fragment::FragSetOP > &  frag_libs)
void protocols::loops::read_loop_fragments ( utility::vector1< core::fragment::FragSetOP > &  frag_libs)
void protocols::loops::remove_cutpoint_variants ( core::pose::Pose pose,
bool  force 
)

Remove cutpoint variants.

Remove cutpoint variants

References core::pose::Pose::constraint_set(), core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::num_cutpoint(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::forge::remodel::RemodelLoopMover::abinitio_stage(), protocols::rbsegment_relax::MakeStarTopologyMover::apply(), protocols::enzdes::BackboneSampler::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::antibody::GraftedStemOptimizer::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::antibody_legacy::AntibodyModeler::apply(), protocols::antibody::LHRepulsiveRampLegacy::apply(), protocols::antibody::RefineOneCDRLoop::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::simple_moves::WobbleMover::apply_fragment(), protocols::antibody::AntibodyCDRGrafter::apply_to_cdr(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::forge::components::BDR::design_refine(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::CDRsMinPackMin::finalize_setup(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::rbsegment_relax::OptimizeThreadingMover::rebuild_unaligned(), protocols::antibody::design::GeneralAntibodyModeler::relax_cdrs(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::antibody::design::AntibodyDesignMover::run_graft(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::forge::remodel::RemodelLoopMover::set_segment_stage(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), and protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol().

void protocols::loops::remove_missing_density ( core::pose::Pose pose,
Loop const &  loop 
)

Rebuild a loop via fragment insertion + ccd closure + minimization

References set_extended_torsions(), and set_single_loop_fold_tree().

Loops protocols::loops::remove_short_chunks ( protocols::loops::Loops const &  input_chunks,
core::Size  minimum_length_of_chunk 
)
Loops protocols::loops::remove_small_gaps ( protocols::loops::Loops const &  input_chunks,
core::Size  gap_size 
)

If two chunks are separated by a small gap of size <= <gap_size>, combine them.

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::num_loop(), protocols::loops::Loop::set_stop(), and stop.

Referenced by extract_secondary_structure_chunks().

void protocols::loops::safe_set_extended_torsions_and_idealize_loops ( const protocols::loops::Loops loops,
core::pose::Pose pose 
)

Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops.

References protocols::loops::Loops::empty(), and set_extended_torsions_and_idealize_loops().

void protocols::loops::select_loop_frags ( loops::Loops const &  loops,
core::fragment::FragSet source,
core::fragment::FragSet loop_frags,
Size  shorten 
)
void protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loops const &  loops,
bool const  include_neighbors,
utility::vector1< bool > &  map,
Real  neighbor_dist 
)

mark loop residues and its neighbors as necessary in a sequence map.

use 10A CB distance cutoff as neighboring residue defintion. The function is used for conveniently setting up sidechain movable residues in loop modeling. The 10A residue set is further reduced if neighbor_dist < 10.0

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References core::select::fill_tenA_neighbor_residues(), filter_loop_neighbors_by_distance(), core::chemical::ResidueType::is_disulfide_bonded(), core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by protocols::antibody::AntibodyInfo::add_CDR_to_MoveMap(), protocols::antibody::LHSnugFitLegacy::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::antibody::H3RefineCCD::apply(), protocols::antibody::task_operations::RestrictToCDRsAndNeighbors::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::simple_task_operations::RestrictToLoops::apply_helper(), protocols::antibody::RefineBetaBarrel::finalize_setup(), protocols::antibody::LHRepulsiveRampLegacy::finalize_setup(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::antibody::design::GeneralAntibodyModeler::get_cdrs_movemap_with_overhang(), protocols::loop_modeler::LoopModeler::get_default_task_factory(), protocols::antibody::AntibodyInfo::get_MoveMap_for_AllCDRsSideChains_and_H3backbone(), protocols::antibody::AntibodyInfo::get_MoveMap_for_Loops(), protocols::antibody::AntibodyInfo::get_TaskFactory_AllCDRs(), protocols::antibody::AntibodyInfo::get_TaskFactory_OneCDR(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::antibody_legacy::AntibodyModeler::relax_cdrs(), protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_rottrials_from_kic_segment(), protocols::antibody::snugdock::SnugDock::setup_objects(), protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors().

utility::vector1< bool > protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loops const &  loops,
bool const  include_neighbors,
Real  neighbor_dist 
)

mark loop residues and its neighbors as necessary in a sequence map.

use 10A CB distance cutoff as neighboring residue defintion. The function is used for conveniently setting up sidechain movable residues in loop modeling. The 10A residue set is further reduced if neighbor_dist < 10.0

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References select_loop_residues(), and core::pose::Pose::size().

void protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loop const &  loop,
bool const  include_neighbors,
utility::vector1< bool > &  map,
Real  neighbor_dist 
)

mark loop residues and its neighbors as necessary for one loop.

for one loop only

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References protocols::loops::Loops::add_loop(), and select_loop_residues().

utility::vector1< bool > protocols::loops::select_loop_residues ( pose::Pose const &  pose,
Loop const &  loop,
bool const  include_neighbors,
Real  neighbor_dist 
)

mark loop residues and its neighbors as necessary for one loop.

for one loop only

Uses 10A neighbor graph for neighbors THEN takes distance from selection to neighbors to trim neighbors. Excludes disulfide residues.

References core::pose::Pose::size().

Referenced by loops_set_move_map(), and select_loop_residues().

void protocols::loops::set_extended_torsions ( core::pose::Pose pose,
Loop const &  loop 
)
void protocols::loops::set_extended_torsions_and_idealize_loops ( core::pose::Pose pose,
loops::Loops  loops 
)
void protocols::loops::set_loop_cutpoint_in_pose_fold_tree ( Size const  new_cutpoint,
pose::Pose pose,
Size const  loop_begin,
Size const  loop_end 
)
void protocols::loops::set_move_map_for_centroid_loop ( Loop const &  loop,
core::kinematics::MoveMap mm 
)
bool protocols::loops::set_secstruct_from_dssp ( pose::Pose pose,
std::string const &  filename 
)

another helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a DSSP file and set that to a Pose. (Rhiju's copy of Chu's psipred reader). Chu, should these functions be moved somewhere to core, along with pdb readers, etc?

References protocols::cluster::calibur::aa, core::pose::Pose::aa(), core::chemical::oneletter_code_from_aa(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and tt().

Referenced by protocols::loop_build::LoopBuildMover::apply(), and protocols::comparative_modeling::initialize_ss().

bool protocols::loops::set_secstruct_from_psipred_ss2 ( pose::Pose pose,
std::string const &  filename 
)

helper function to set secondary structure of a Pose from an external file.

read in secondary structure definition from a psipred_ss2 file and set that to a Pose. A temporary setup since there is very limited ss support in Pose right now.

References core::pose::read_psipred_ss2_file(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::set_ss_from_phipsi(), and tt().

Referenced by protocols::loop_build::LoopBuildMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::LoopRebuild::apply(), protocols::comparative_modeling::initialize_ss(), and protocols::hybridization::FoldTreeHybridize::setup_foldtree().

void protocols::loops::set_single_loop_fold_tree ( core::pose::Pose pose,
Loop const &  loop 
)
Loops protocols::loops::split_by_ca_ca_dist ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  input_chunks,
core::Real const  CA_CA_distance_cutoff 
)
Loops protocols::loops::split_by_resSeq ( core::pose::Pose const &  pose)
Loops protocols::loops::split_by_resSeq ( core::pose::Pose const &  pose,
protocols::loops::Loops const &  input_chunks 
)
static basic::Tracer protocols::loops::TR ( "protocols.loops.FoldTreeFromLoopsWrapper"  )
static
static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopsFileIO"  )
static
static basic::Tracer protocols::loops::TR ( "protocols.loops.make_loops"  ,
t_info   
)
static
static basic::Tracer protocols::loops::tr ( "protocols.loops.Loop"  )
static
static basic::Tracer protocols::loops::tr ( "protocols.loops.LoopMoverFactory"  )
static
static basic::Tracer protocols::loops::tr ( "loops"  )
static
void protocols::loops::trim_back_sequence_mapping ( id::SequenceMapping mapping,
std::string const &  source_seq,
std::string const &  target_seq,
Size const  min_loop_size 
)

Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.

Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed.

References protocols::mean_field::min(), core::id::SequenceMapping::reverse(), core::id::SequenceMapping::size1(), core::id::SequenceMapping::size2(), and tt().

static basic::Tracer protocols::loops::tt ( "protocols.loops.loops_main"  )
static
void protocols::loops::validate_loop_start_stop ( bool  prohibit_single_residue_loops,
core::Size  start,
core::Size  stop,
std::string const &  filename,
core::Size  linecount 
)

Checks if there is a problem with the beginning and ending residues defined in a loops file.

Referenced by protocols::loops::PoseNumberedLoopFileReader::read_pose_numbered_loops_file(), and protocols::loops::LoopFromFileData::resolve_as_serialized_loop_from_pose().

Variable Documentation

const double protocols::loops::EXT_OMG = 180
static
const double protocols::loops::EXT_PHI = -150
static
const double protocols::loops::EXT_PSI = +150
static